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  title={Conditional segmentation in lieu of image registration},
  author={Hu, Yipeng and Gibson, Eli and Barratt, Dean C and Emberton, Mark and Noble, J Alison and Vercauteren, Tom},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={401--409},
  year={2019},
  doi={10.1007/978-3-030-32245-8_45},
  organization={Springer}
}

@article{hu2018weakly,
  title={Weakly-supervised convolutional neural networks for multimodal image registration},
  author={Hu, Yipeng and Modat, Marc and Gibson, Eli and Li, Wenqi and Ghavami, Nooshin and Bonmati, Ester and Wang, Guotai and Bandula, Steven and Moore, Caroline M and Emberton, Mark and others},
  journal={Medical image analysis},
  volume={49},
  pages={1--13},
  year={2018},
  doi={10.1016/j.media.2018.07.002},
  publisher={Elsevier}
}

@inproceedings{hu2018label,
  title={Label-driven weakly-supervised learning for multimodal deformable image registration},
  author={Hu, Yipeng and Modat, Marc and Gibson, Eli and Ghavami, Nooshin and Bonmati, Ester and Moore, Caroline M and Emberton, Mark and Noble, J Alison and Barratt, Dean C and Vercauteren, Tom},
  booktitle={2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)},
  pages={1070--1074},
  year={2018},
  doi={10.1109/ISBI.2018.8363756},
  organization={IEEE}
}

@article{de2019deep,
  title={A deep learning framework for unsupervised affine and deformable image registration},
  author={de Vos, Bob D and Berendsen, Floris F and Viergever, Max A and Sokooti, Hessam and Staring, Marius and I{\v{s}}gum, Ivana},
  journal={Medical image analysis},
  volume={52},
  pages={128--143},
  year={2019},
  doi={10.1016/j.media.2018.11.010},
  publisher={Elsevier}
}

@article{balakrishnan2019voxelmorph,
  title={VoxelMorph: a learning framework for deformable medical image registration},
  author={Balakrishnan, Guha and Zhao, Amy and Sabuncu, Mert R and Guttag, John and Dalca, Adrian V},
  journal={IEEE transactions on medical imaging},
  volume={38},
  number={8},
  pages={1788--1800},
  year={2019},
  doi={10.1109/TMI.2019.2897538},
  publisher={IEEE}
}

@article{dalca2019unsupervised,
  title={Unsupervised learning of probabilistic diffeomorphic registration for images and surfaces},
  author={Dalca, Adrian V and Balakrishnan, Guha and Guttag, John and Sabuncu, Mert R},
  journal={Medical image analysis},
  volume={57},
  pages={226--236},
  year={2019},
  doi={10.1016/j.media.2019.07.006},
  publisher={Elsevier}
}

@misc{yang2020longitudinal,
    title={Longitudinal Image Registration with Temporal-order and Subject-specificity Discrimination},
    author={Qianye Yang and Yunguan Fu and Francesco Giganti and Nooshin Ghavami and Qingchao Chen and J. Alison Noble and Tom Vercauteren and Dean Barratt and Yipeng Hu},
    year={2020},
    eprint={2008.13002},
    archivePrefix={arXiv},
    primaryClass={eess.IV},
    doi={10.1007/978-3-030-59716-0_24}
}

@article{gibson2018niftynet,
  title={NiftyNet: a deep-learning platform for medical imaging},
  author={Gibson, Eli and Li, Wenqi and Sudre, Carole and Fidon, Lucas and Shakir, Dzhoshkun I and Wang, Guotai and Eaton-Rosen, Zach and Gray, Robert and Doel, Tom and Hu, Yipeng and others},
  journal={Computer methods and programs in biomedicine},
  volume={158},
  pages={113--122},
  year={2018},
  doi={10.1016/j.cmpb.2018.01.025},
  publisher={Elsevier}
}

@inproceedings{he2016deep,
  title={Deep residual learning for image recognition},
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  year={2016},
  doi={10.1109/CVPR.2016.90}
}

@article{simonyan2014very,
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}

@article{ashburner2007fast,
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@article{vercauteren2009diffeomorphic,
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@article{brown2020introduction,
  title={Introduction to Medical Image Registration with DeepReg, between Old and New},
  author={Montana Brown, Nina and Fu, Yunguan and Saeed, Shaheer U. and Casamitjana, Adrià and Baum, Zachary M. C. and Delaunay, Rémi and Yang, Qianye and Grimwood, Alexander and Min, Zhe and Bonmati, Ester and Vercauteren, Tom and Clarkson, Matthew J. and Hu, Yipeng},
  url={https://github.com/DeepRegNet/DeepReg/blob/main/docs/Intro_to_Medical_Image_Registration.ipynb},
  year={2020}
}

@article{zhuang2020cardiac,
  title={Cardiac segmentation on late gadolinium enhancement mri: A benchmark study from multi-sequence cardiac mr segmentation challenge},
  author={Zhuang, Xiahai and Xu, Jiahang and Luo, Xinzhe and Chen, Chen and Ouyang, Cheng and Rueckert, Daniel and Campello, Victor M and Lekadir, Karim and Vesal, Sulaiman and RaviKumar, Nishant and others},
  journal={arXiv preprint arXiv:2006.12434},
  year={2020}
}

@article{hill2001medical,
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@article{haskins2020deep,
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  publisher={Springer}
}

@article{fu2020deep,
  title={Deep learning in medical image registration: a review},
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}

@article{luo2020mvmm,
  title={MvMM-RegNet: A new image registration framework based on multivariate mixture model and neural network estimation},
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  year={2020},
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}

@inproceedings{dalca2019learning,
  title={Learning conditional deformable templates with convolutional networks},
  author={Dalca, Adrian and Rakic, Marianne and Guttag, John and Sabuncu, Mert},
  booktitle={Advances in neural information processing systems},
  pages={806--818},
  year={2019}
}

@incollection{siebert2020deep,
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  booktitle={Bildverarbeitung f{\"u}r die Medizin 2020},
  pages={236--241},
  year={2020},
  doi={10.1007/978-3-658-29267-6_53},
  publisher={Springer}
}

@article{rueckert1999nonrigid,
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@dataset{hering_alessa_2020_3835682,
  author = {Hering, Alessa and Murphy,Keelin and van Ginneken, Bram},
  title = {{Lean2Reg Challenge: CT Lung Registration - Training Data}},
  month = may,
  year = 2020,
  publisher = {Zenodo},
  doi = {10.5281/zenodo.3835682},
  url = {https://doi.org/10.5281/zenodo.3835682}
}

@article{xiao2017resect,
  title={REtroSpective Evaluation of Cerebral Tumors (RESECT): A clinical database of pre-operative MRI and intra-operative ultrasound in low-grade glioma surgeries},
  author={Xiao, Yiming and Fortin, Maryse and Unsg{\aa}rd, Geirmund and Rivaz, Hassan and Reinertsen, Ingerid},
  journal={Medical physics},
  volume={44},
  number={7},
  pages={3875--3882},
  year={2017},
  doi={10.1002/mp.12268},
  publisher={Wiley Online Library}
}

@misc{adrian_dalca_2020_3715652,
  author       = {Adrian Dalca and
                  Yipeng Hu and
                  Tom Vercauteren and
                  Mattias Heinrich and
                  Lasse Hansen and
                  Marc Modat and
                  Bob de Vos and
                  Yiming Xiao and
                  Hassan Rivaz and
                  Matthieu Chabanas and
                  Ingerid Reinertsen and
                  Bennett Landman and
                  Jorge Cardoso and
                  Bram van Ginneken and
                  Alessa Hering and
                  Keelin Murphy},
  title        = {Learn2Reg - The Challenge},
  month        = mar,
  year         = 2020,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.3715652},
  url          = {https://doi.org/10.5281/zenodo.3715652}
}

@article{simpson2019large,
  title={A large annotated medical image dataset for the development and evaluation of segmentation algorithms},
  author={Simpson, Amber L and Antonelli, Michela and Bakas, Spyridon and Bilello, Michel and Farahani, Keyvan and Van Ginneken, Bram and Kopp-Schneider, Annette and Landman, Bennett A and Litjens, Geert and Menze, Bjoern and others},
  journal={arXiv preprint arXiv:1902.09063},
  year={2019}
}

@article{modat2010fast,
  title={Fast free-form deformation using graphics processing units},
  author={Modat, Marc and Ridgway, Gerard R and Taylor, Zeike A and Lehmann, Manja and Barnes, Josephine and Hawkes, David J and Fox, Nick C and Ourselin, S{\'e}bastien},
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  publisher={Elsevier},
  doi={10.1016/j.cmpb.2009.09.002}
}

@article{marstal2016simpleelastix,
  title={SimpleElastix: A user-friendly, multi-lingual library for medical image registration},
  author={Marstal, Kasper and Berendsen, Floris and Staring, Marius and Klein, Stefan},
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  pages={134--142},
  year={2016},
  doi={10.1109/CVPRW.2016.78}
}

@article{sandkuhler2018airlab,
  title={AirLab: autograd image registration laboratory},
  author={Sandk{\"u}hler, Robin and Jud, Christoph and Andermatt, Simon and Cattin, Philippe C},
  journal={arXiv preprint arXiv:1806.09907},
  year={2018}
}

@misc{tensorflow2015-whitepaper,
title={ {TensorFlow}: Large-Scale Machine Learning on Heterogeneous Systems},
url={https://www.tensorflow.org/},
note={Software available from tensorflow.org},
author={
    Mart\'{\i}n~Abadi and
    Ashish~Agarwal and
    Paul~Barham and
    Eugene~Brevdo and
    Zhifeng~Chen and
    Craig~Citro and
    Greg~S.~Corrado and
    Andy~Davis and
    Jeffrey~Dean and
    Matthieu~Devin and
    Sanjay~Ghemawat and
    Ian~Goodfellow and
    Andrew~Harp and
    Geoffrey~Irving and
    Michael~Isard and
    Yangqing Jia and
    Rafal~Jozefowicz and
    Lukasz~Kaiser and
    Manjunath~Kudlur and
    Josh~Levenberg and
    Dandelion~Man\'{e} and
    Rajat~Monga and
    Sherry~Moore and
    Derek~Murray and
    Chris~Olah and
    Mike~Schuster and
    Jonathon~Shlens and
    Benoit~Steiner and
    Ilya~Sutskever and
    Kunal~Talwar and
    Paul~Tucker and
    Vincent~Vanhoucke and
    Vijay~Vasudevan and
    Fernanda~Vi\'{e}gas and
    Oriol~Vinyals and
    Pete~Warden and
    Martin~Wattenberg and
    Martin~Wicke and
    Yuan~Yu and
    Xiaoqiang~Zheng},
  year={2015},
}
